Edit: Go figure, as soon as I posted this, I saw 4 ships of the damned. However, the spawn rates seem a lot lower than they used to be. I used to see them all the time as soon as I left the coast an of island. Now I get lucky if I see a handful in the middle of the ocean
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When I first started this new single player run-through on Blackwood, everything worked fine. A few days later, I noticed there were no longer any ships of the damned.